Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (adenine(58)-N(1))-methyltransferase TrmI
Synonym: TT_C0244
GI: 46198552
COG: COG2519
UniProt: Q8GBB2
Structures: | 2PWY | 5C0O | 5C1I |
Alpha Fold Predicted Structure: AF-Q8GBB2-F1
Enzyme type: methyltransferase
Position of modification - modification: t:58 - m1A


PDB Structures:


2PWY

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed.

Download RCSB-PDB Structures:

Pdb Files   5C0O.pdb   5C1I.pdb   5IL2.pdb  
Pdbx/mmCIF Files   5C0O.cif   5C1I.cif   5IL2.cif  


Protein sequence:

MAWPGPLLLKDRKGRAYLVFPKEGGVFHHHKGSVPHEALLEAGPGGVVRTHLGEELSVHRPTLEEYLLHMKRSATPTYPKDASAMVTLLDLAPGMRVLEAGTGSGGLTLFLARAVGEKGLVESYEARPHHLAQAERNVRAFWQVENVRFHLGKLEEAELEEAAYDGVALDLMEPWKVLEKAALALKPDRFLVAYLPNITQVLELVRAAEAHPFRLERVLEVGWREWEVRLPVAHPRFQQVGHTAFLVALRRWKAS

Comments:

Homologous to M. tuberculosis Rv2118c.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m1A RNA tRNA 58 GUC GUC tRNAAspGUC TΨC-loop Prokaryotic Cytosol 12682365   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M A W P G P L L L K D R K G R A Y L V F P K E G G V F H H H K G S V P H E A L L E A G P G G V V R T H L G E E L S V H R P T L E E Y L L H M K R S A T P T Y P K D A S A M V T L L D L A P G M R V L E A G T G S G G L T L F L A R A V G E K G L V E S Y E A R P H H L A Q A E R N V R A F W Q V E N V R F H L G K L E E A E L E E A A Y D G V A L D L M E P W K V L E K A A L A L K P D R F L V A Y L P N I T Q V L E L V R A A E A H P F R L E R V L E V G W R E W E V R L P V A H P R F Q Q V G H T A F L V A L R R W K A S

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q8GBB2-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q8GBB2-F1.cif  
DSSP Secondary Structures   Q8GBB2.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural comparison of tRNA m(1)A58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions. Guelorget A, Barraud P, Tisne C, Golinelli-Pimpaneau B BMC Struct Biol [details] 22168821 -
Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H Nucleic Acids Res [details] 12682365 -
Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA. Barraud P, Golinelli-Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, Dardel F, Tisne C J Mol Biol [details] 18262540 -
Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI). Takuma H, Ushio N, Minoji M, Kazayama A, Shigi N, Hirata A, Tomikawa C, Ochi A, Hori H J Biol Chem. [details] 25593312 10.1074/jbc.M114.606038